Locus 4092

Sequence ID 2R_DroMel_CAF1
Location 13,482,531 – 13,482,668
Length 137
Max. P 0.604994
window6588 window6589 window6590

overview

Window 8

Location 13,482,531 – 13,482,634
Length 103
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 84.45
Mean single sequence MFE -26.57
Consensus MFE -16.14
Energy contribution -17.17
Covariance contribution 1.03
Combinations/Pair 1.14
Mean z-score -2.88
Structure conservation index 0.61
SVM decision value -0.05
SVM RNA-class probability 0.509532
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13482531 103 + 20766785
-------AAAAGUUGGAAUAAAGAAAAACAA-AAGGCAGCGGAAUGAGAUGAUAAACUUGGAUUUAACCUGCCAACGGGAAUAAUCCCGAAGGACAUAAGUCCU-UAGC------UGG
-------...((((.................-..(((((..(((((((........)))..))))...)))))..(((((....)))))((((((....)))))-))))------).. ( -25.50)
>DroSec_CAF1 31198 104 + 1
-------AAAAGUUGGAACAAAGAAAAACAAAAAGGCAGCGGAAUGAGAUGAUAAACUUGGAUUUAACCUGCCAACGGGAAUAAUCCCGAAGGACAUAAGUCCU-UUGC------UGA
-------.............................(((((((..(((........)))(((((((...((((..(((((....)))))..)).))))))))))-))))------)). ( -24.70)
>DroSim_CAF1 31346 104 + 1
-------AAAAGUUGGAACAAAGAAAAACAAAAAGGCAGCGGAAUGAGAUGAUAAACUUGGAUUUAACCUGCCAACGGGAAUAAUCCCGAAGGACAUAAGUCCU-UUGC------UGA
-------.............................(((((((..(((........)))(((((((...((((..(((((....)))))..)).))))))))))-))))------)). ( -24.70)
>DroEre_CAF1 31571 103 + 1
-------AAAAGUUGGAACAAAGAAAAACAA-AAGGCAGCGGAAUGGGAUGAUAAACUUGGGUUUAACCUGCCAACGGGAAUAAUCCCGAAGGACAUAAGUCCU-UUGC------UGU
-------........................-...(((((.....(((((..(((((....))))).((((....))))....)))))(((((((....)))))-))))------))) ( -29.40)
>DroYak_CAF1 32726 116 + 1
AAAAAAAAAAAGUUGGAACAAAGAAAAACAA-AAGGCAGCGGCAGGGGAUGAUAAACUUGGAUUUAACCUGCCAACGGGAAUAAUCCCGAAGGACAAAAGUCCU-UUGCUUUUACUGU
..............................(-((((((..((((((....(((........)))...))))))..(((((....)))))((((((....)))))-))))))))..... ( -32.50)
>DroAna_CAF1 32565 103 + 1
-------AAAAGUUAAAAGAAAGAAGACUGGGAAAGC--UGGGAUGAGAGGUUUAACUUGGAUAUAACCUGCCAGCGGAUAUAAUCCCGGCGGAGAUAAGUUCUUUUGU------UGU
-------...........((((((..(((......((--((((((..(((......)))...((((.((.......)).)))))))))))).......)))))))))..------... ( -22.62)
>consensus
_______AAAAGUUGGAACAAAGAAAAACAA_AAGGCAGCGGAAUGAGAUGAUAAACUUGGAUUUAACCUGCCAACGGGAAUAAUCCCGAAGGACAUAAGUCCU_UUGC______UGU
..................................(((((..(((((((........)))..))))...)))))..(((((....)))))..((((....))))............... (-16.14 = -17.17 +   1.03)

alignment

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secondary structure

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Window 9

Location 13,482,531 – 13,482,634
Length 103
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 84.45
Mean single sequence MFE -22.52
Consensus MFE -14.78
Energy contribution -15.33
Covariance contribution 0.56
Combinations/Pair 1.14
Mean z-score -2.44
Structure conservation index 0.66
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13482531 103 - 20766785
CCA------GCUA-AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCUCAUUCCGCUGCCUU-UUGUUUUUCUUUAUUCCAACUUUU-------
(((------((.(-(((((....)))))).((((....))))))))).((((........((........)).........)))).-........................------- ( -20.93)
>DroSec_CAF1 31198 104 - 1
UCA------GCAA-AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCUCAUUCCGCUGCCUUUUUGUUUUUCUUUGUUCCAACUUUU-------
..(------((((-(((((....))))..(((((....)))))..(((((.............................)))))..))))))...................------- ( -21.55)
>DroSim_CAF1 31346 104 - 1
UCA------GCAA-AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCUCAUUCCGCUGCCUUUUUGUUUUUCUUUGUUCCAACUUUU-------
..(------((((-(((((....))))..(((((....)))))..(((((.............................)))))..))))))...................------- ( -21.55)
>DroEre_CAF1 31571 103 - 1
ACA------GCAA-AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAACCCAAGUUUAUCAUCCCAUUCCGCUGCCUU-UUGUUUUUCUUUGUUCCAACUUUU-------
.((------((.(-(((((....))))))(((((....))))).(((...(.(((((....))))).)...)))....))))....-........................------- ( -24.80)
>DroYak_CAF1 32726 116 - 1
ACAGUAAAAGCAA-AGGACUUUUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCCCCUGCCGCUGCCUU-UUGUUUUUCUUUGUUCCAACUUUUUUUUUUU
((((.((((((((-(((((....))))..(((((....)))))..((((((.(((((....)))))......)))))).......)-))))))))..))))................. ( -30.50)
>DroAna_CAF1 32565 103 - 1
ACA------ACAAAAGAACUUAUCUCCGCCGGGAUUAUAUCCGCUGGCAGGUUAUAUCCAAGUUAAACCUCUCAUCCCA--GCUUUCCCAGUCUUCUUUCUUUUAACUUUU-------
...------..(((((((.............((((...))))(((((.(((((............)))))......)))--))..............))))))).......------- ( -15.80)
>consensus
ACA______GCAA_AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCUCAUUCCGCUGCCUU_UUGUUUUUCUUUGUUCCAACUUUU_______
...............((((....))))..(((((....)))))..(((((.............................))))).................................. (-14.78 = -15.33 +   0.56)

alignment

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secondary structure

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Window 0

Location 13,482,561 – 13,482,668
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.50
Mean single sequence MFE -22.75
Consensus MFE -14.19
Energy contribution -14.42
Covariance contribution 0.22
Combinations/Pair 1.12
Mean z-score -2.07
Structure conservation index 0.62
SVM decision value 0.14
SVM RNA-class probability 0.604994
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13482561 107 - 20766785
UAUUUUCGUCCAAUA------CAAGUACAAAUACCUACAGCCA------GCUA-AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCUCAUUCCGC
...............------...........((((...((((------((.(-(((((....)))))).((((....))))))))))))))............................ ( -26.10)
>DroSec_CAF1 31229 107 - 1
UAUUUUCGUCCAAUA------CAAGUACAAAUACCUACAGUCA------GCAA-AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCUCAUUCCGC
...............------...........((((...((((------((.(-(((((....)))))).((((....))))))))))))))............................ ( -24.00)
>DroSim_CAF1 31377 107 - 1
UAUUUUCGUCCAAUA------CAAGUACAAAUACCUACAGUCA------GCAA-AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCUCAUUCCGC
...............------...........((((...((((------((.(-(((((....)))))).((((....))))))))))))))............................ ( -24.00)
>DroEre_CAF1 31601 106 - 1
UAUUUUU-UCCAAUC------CAAGUGCAAAUACCUACACACA------GCAA-AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAACCCAAGUUUAUCAUCCCAUUCCGC
.......-.......------.....((....((((.....((------((.(-(((((....)))))).((((....))))))))..))))(((((....)))))............)) ( -22.20)
>DroYak_CAF1 32763 118 - 1
UAUUUUU-UCCAAUUUAAGUACAAGUACAAAUACAUACACACAGUAAAAGCAA-AGGACUUUUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCCCCUGCCGC
.......-..........(((....))).....................((.(-(((((....))))))(((((....)))))..((((((.(((((....)))))......)))))))) ( -27.00)
>DroAna_CAF1 32595 110 - 1
UUUGUUU-UUCAAAUCAAAUAAAA--AUAAAAACCUACACACA------ACAAAAGAACUUAUCUCCGCCGGGAUUAUAUCCGCUGGCAGGUUAUAUCCAAGUUAAACCUCUCAUCCCA-
(((((((-((..........))))--)))))(((((.......------.....(((.....)))..((((((........).))))))))))..........................- ( -13.20)
>consensus
UAUUUUC_UCCAAUA______CAAGUACAAAUACCUACACACA______GCAA_AGGACUUAUGUCCUUCGGGAUUAUUCCCGUUGGCAGGUUAAAUCCAAGUUUAUCAUCUCAUUCCGC
.......................................................((((((.((((...(((((....)))))..))))((......))))))))............... (-14.19 = -14.42 +   0.22)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:35 2006